lamindb

Track biological data lineage with ontology-aware annotations via Bionty.

1|Updated Mar 4, 2026
One-click install
npx skills add https://github.com/Hung-3008/agusta --skill lamindb-hung-3008
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: lamindb
Source: https://github.com/Hung-3008/agusta/tree/main/.agents/skills/lamindb
Command: npx skills add https://github.com/Hung-3008/agusta --skill lamindb-hung-3008

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill includes references (resource) components.

What problem does it solve?

LaminDB resolves the challenge of organizing, validating, and reproducing complex biological data by providing end-to-end lineage tracking and ontology-aware metadata management.

Core Features & Use Cases

  • Ontology-driven curation and annotation of biological datasets (cell types, tissues, diseases)
  • Full data lineage tracking across artifacts, runs, and transforms
  • Schema-based validation and standardization to ensure reproducibility

Quick Start

Start tracking with LaminDB and load a dataset to begin ontology-enabled curation.

Frequently Asked Questions about lamindb

High-intent search queries and answers about installing and using this skill.

FAQPage Schema
How do I track data lineage and reproduce scRNA-seq analysis runs?▼

Track scRNA-seq data lineage by linking artifacts, runs, and transforms to create traceable workflows. This schema-based validation ensures biological data analysis is fully reproducible and auditable across multi-omics experiments.

What is ontology-aware annotation for biological data management?▼

Ontology-aware annotation standardizes biological metadata by mapping cell types, tissues, and diseases to controlled vocabularies via Bionty. This validation ensures datasets remain consistent, searchable, and interoperable across complex multi-omics workflows.

Can I use LaminDB for curating spatial transcriptomics and flow cytometry datasets?▼

LaminDB supports spatial transcriptomics, flow cytometry, and scRNA-seq workflows for data curation. You can apply ontology-driven annotation and track full data lineage across these diverse biological data modalities to ensure reproducible research.

How does biological data lineage tracking compare to general data management?▼

Biological data lineage tracking captures experiment-specific transforms and runs, whereas general data management only stores files. This approach provides end-to-end provenance and ontology-aware validation specifically for complex multi-omics workflows.

Does LaminDB integrate with existing workflow tools for multi-omics data validation?▼

LaminDB offers flexible deployment options and workflow tool integrations for multi-omics data validation. It connects your existing pipeline transforms to tracked artifacts, maintaining complete provenance without disrupting your established analysis environment.

When should I use schema-based validation for biological datasets?▼

Use schema-based validation when standardizing complex biological datasets to ensure reproducibility. It enforces ontology-aware metadata structures across artifacts and transforms, preventing annotation errors before they propagate through downstream analysis.